SirB - PFAM28P - GREMLIN Contacts

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SirB - Invasion gene expression up-regulator, SirB

PFAM:	PF04247	Sequences: YLALKHLHVTAVALSGALFVLRGLWMLAGSPWLQARWVRILPHVIDTLLLASAIALAVILGQYPFVQGWLTAKLVLLVVYIVLGTIALKRGRTRRVRAAAFLAALAVFAYIVSVALTKSP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	120 (120)
Sequences:	5074 (3771)
Seq/√Len:	344.2
META:	0.851

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
23_G	101_F	3.213	1.00
16_G	108_F	3.118	1.00
11_A	48_L	2.487	1.00
4_L	55_A	2.264	1.00
86_I	100_A	2.032	1.00
83_L	107_V	1.953	1.00
25_W	38_V	1.948	1.00
85_T	90_R	1.912	1.00
36_R	40_I	1.905	1.00
9_V	12_V	1.895	1.00
85_T	89_K	1.851	1.00
54_I	58_V	1.839	1.00
11_A	45_I	1.821	1.00
76_L	110_Y	1.812	1.00
6_H	10_T	1.777	1.00
21_L	25_W	1.717	1.00
7_L	11_A	1.706	1.00
83_L	103_A	1.695	1.00
77_L	111_I	1.694	1.00
2_L	6_H	1.598	1.00
94_R	98_A	1.572	1.00
51_A	55_A	1.568	1.00
29_G	94_R	1.557	1.00
110_Y	113_S	1.544	1.00
27_L	98_A	1.507	1.00
79_V	107_V	1.502	1.00
25_W	32_W	1.464	1.00
55_A	59_I	1.460	1.00
82_V	85_T	1.456	1.00
91_G	96_V	1.454	1.00
110_Y	114_V	1.440	1.00
45_I	52_S	1.433	1.00
14_L	45_I	1.410	1.00
76_L	111_I	1.403	1.00
37_W	41_L	1.365	1.00
63_Y	71_T	1.361	1.00
24_L	28_A	1.361	1.00
25_W	30_S	1.355	1.00
65_F	71_T	1.353	1.00
103_A	107_V	1.352	1.00
90_R	93_T	1.350	1.00
4_L	59_I	1.337	1.00
62_Q	71_T	1.314	1.00
16_G	105_L	1.269	1.00
26_M	33_L	1.268	1.00
3_A	6_H	1.264	1.00
13_A	17_A	1.263	1.00
63_Y	66_V	1.258	1.00
32_W	35_A	1.258	1.00
53_A	74_L	1.246	1.00
7_L	48_L	1.204	1.00
72_A	76_L	1.140	1.00
25_W	33_L	1.139	1.00
96_V	100_A	1.127	1.00
20_V	101_F	1.121	1.00
82_V	86_I	1.118	1.00
26_M	94_R	1.115	1.00
53_A	57_A	1.097	1.00
95_R	99_A	1.093	1.00
9_V	13_A	1.086	1.00
57_A	63_Y	1.084	1.00
112_V	116_L	1.071	1.00
57_A	71_T	1.043	1.00
35_A	38_V	1.028	1.00
101_F	105_L	1.014	1.00
57_A	60_L	1.012	1.00
40_I	44_V	1.007	1.00
20_V	105_L	0.998	1.00
5_K	9_V	0.984	1.00
40_I	43_H	0.975	1.00
26_M	88_L	0.955	1.00
83_L	100_A	0.955	1.00
15_S	80_Y	0.951	1.00
16_G	20_V	0.945	1.00
105_L	109_A	0.939	1.00
26_M	97_R	0.937	1.00
20_V	24_L	0.934	1.00
26_M	91_G	0.928	1.00
62_Q	67_Q	0.924	1.00
113_S	119_S	0.917	1.00
46_D	80_Y	0.903	1.00
60_L	67_Q	0.892	1.00
64_P	71_T	0.890	1.00
72_A	77_L	0.888	1.00
23_G	27_L	0.883	1.00
49_L	53_A	0.865	1.00
78_V	81_I	0.860	1.00
113_S	117_T	0.859	1.00
86_I	96_V	0.850	1.00
47_T	51_A	0.843	1.00
21_L	38_V	0.841	1.00
60_L	118_K	0.840	1.00
78_V	82_V	0.833	1.00
61_G	64_P	0.827	1.00
85_T	88_L	0.825	1.00
64_P	67_Q	0.822	1.00
99_A	103_A	0.800	1.00
68_G	71_T	0.783	1.00
76_L	114_V	0.774	1.00
55_A	58_V	0.768	1.00
46_D	50_L	0.765	1.00
41_L	45_I	0.761	1.00
108_F	112_V	0.758	1.00
68_G	72_A	0.751	1.00
114_V	119_S	0.748	1.00
14_L	18_L	0.746	1.00
71_T	75_V	0.745	1.00
93_T	96_V	0.741	1.00
13_A	116_L	0.739	1.00
57_A	64_P	0.730	0.99
7_L	52_S	0.729	0.99
61_G	67_Q	0.728	0.99
13_A	112_V	0.724	0.99
38_V	41_L	0.721	0.99
72_A	110_Y	0.720	0.99
3_A	7_L	0.717	0.99
62_Q	66_V	0.717	0.99
63_Y	67_Q	0.715	0.99
30_S	33_L	0.706	0.99
95_R	98_A	0.697	0.99
32_W	37_W	0.694	0.99
81_I	84_G	0.694	0.99
15_S	46_D	0.692	0.99
96_V	99_A	0.684	0.99
67_Q	71_T	0.682	0.99
92_R	96_V	0.681	0.99
71_T	74_L	0.678	0.99
6_H	9_V	0.678	0.99
18_L	38_V	0.677	0.99
12_V	52_S	0.676	0.99
82_V	90_R	0.662	0.99
17_A	21_L	0.661	0.99
6_H	11_A	0.660	0.99
11_A	52_S	0.657	0.99
28_A	31_P	0.648	0.99
24_L	101_F	0.646	0.99
57_A	62_Q	0.636	0.99
69_W	73_K	0.634	0.98
19_F	87_A	0.634	0.98
6_H	13_A	0.633	0.98
79_V	83_L	0.632	0.98
22_R	46_D	0.615	0.98
100_A	103_A	0.613	0.98
103_A	106_A	0.611	0.98
50_L	53_A	0.610	0.98
16_G	112_V	0.609	0.98
18_L	45_I	0.603	0.98
39_R	46_D	0.600	0.98
63_Y	74_L	0.596	0.98
17_A	108_F	0.595	0.98
98_A	102_L	0.590	0.98
22_R	80_Y	0.589	0.98
109_A	113_S	0.587	0.97
67_Q	70_L	0.584	0.97
66_V	71_T	0.575	0.97
31_P	35_A	0.575	0.97
94_R	97_R	0.571	0.97
6_H	17_A	0.570	0.97
6_H	14_L	0.559	0.97
86_I	91_G	0.558	0.97
10_T	14_L	0.557	0.97
23_G	26_M	0.553	0.96
95_R	106_A	0.551	0.96
15_S	53_A	0.550	0.96
22_R	49_L	0.546	0.96
101_F	107_V	0.543	0.96
10_T	13_A	0.540	0.96
39_R	42_P	0.540	0.96
37_W	42_P	0.527	0.95
34_Q	89_K	0.525	0.95
24_L	27_L	0.522	0.95
99_A	119_S	0.519	0.95
75_V	79_V	0.516	0.95
76_L	107_V	0.515	0.95
99_A	106_A	0.512	0.95
90_R	96_V	0.510	0.94
110_Y	119_S	0.503	0.94
1_Y	56_L	0.503	0.94
12_V	112_V	0.501	0.94
108_F	111_I	0.500	0.94

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
3qbgA	3	0.95	6.8	0.908	Contact Map
4l35A	3	0.5	4.3	0.917	Contact Map
4o6yA	2	0.9667	3.8	0.918	Contact Map
2jafA	3	0.95	3.1	0.922	Contact Map
1xioA	2	0.9333	3	0.923	Contact Map
4p02A	1	0.6333	2.9	0.923	Contact Map
4px7A	1	0.7833	2.1	0.929	Contact Map
3ddlA	2	0.975	2.1	0.929	Contact Map
4m5bA	1	0.4583	2	0.93	Contact Map
4xtlA	1	0.9833	2	0.93	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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